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Optimization of force fields for molecular dynamicsDi Pierro, Michele 09 February 2015 (has links)
A technology for optimization of potential parameters from condensed phase simulations (POP) is discussed and illustrated. It is based on direct calculations of the derivatives of macroscopic observables with respect to the potential parameters. The derivatives are used in a local minimization scheme, comparing simulated and experimental data. In particular, we show that the Newton Trust-Region protocol allows for accurate and robust optimization. POP is illustrated for a toy problem of alanine dipeptide and is applied to folding of the peptide WAAAH. The helix fraction is highly sensitive to the potential parameters while the slope of the melting curve is not. The sensitivity variations make it difficult to satisfy both observations simultaneously. We conjecture that there is no set of parameters that reproduces experimental melting curves of short peptides that are modeled with the usual functional form of a force field. We then apply the newly developed technology to study the liquid mixture of tert-butanol and water. We are able to obtain, after 4 iterations, the correct phase behavior and accurately predict the value of the Kirkwood Buff (KB) integrals. We further illustrate that a potential that is determined solely by KB information, or the pair correlation function, is not necessarily unique. / text
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Schwingungsspektroskopie nah- und überkritischer Lösungsmittel / Vibrational spectroscopy of near- and supercritical solventsAbraham, Sascha 27 June 2013 (has links)
Expansionen komprimierter Fluide finden breite Anwendung und werden hier mit Hilfe der Schwingungsspektroskopie untersucht. Dabei ist der Aggregatzustand der bei der Zerstäubung entstehenden Partikel von besonderem Interesse. In Abhängigkeit von Stagnationsdruck, Düsentemperatur, und Düsenabstand werden neben Lachgas tert-Butylalkohol und n-Pentan hinsichtlich ihrer Partikelbildung charakterisiert. Die Ergebnisse bilden eine Grundlage für die Expansion nahkritischer Lösungen.
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Caractérisation moléculaire des adénomes hépatocytaires et des lésions prénéoplasiques hépatiques / Molecular characterization of hepatocellular adenomas and hepatic preneoplastic lesionsCalderaro, Julien 30 October 2014 (has links)
Première partie: Les adénomes hépatocellulaires (AHC) sont des tumeurs bénignes qui se développent le plus souvent chez la femme jeune suite à la prise de contraceptifs oraux. Ils sont classés, sur le plan moléculaire, en: 1) AHC inflammatoires (AHCI), caractérisés par des mutations de différents gènes (IL6ST, GNAS ou STAT3) entrainant une activation de la voie de signalisation de l'interleukine 6; 2) les AHC avec mutations biallèliques inactivatrices d'HNF1A (H-AHC); 3) les AHC mutés pour CTNNB1 (bAHC) qui présentent un risque accru de transformation maligne et 4) les AHC non classés (UAHC). La glycogénose de type I (GSD I) est une maladie métabolique héréditaire rare qui prédispose au développement des AHC. Cependant les principales études moléculaires des AHC ont été réalisées sur des tumeurs sporadiques, et le profil moléculaire des AHC associée à la GSDI reste à déterminer.L'objectif de notre a été de caractériser, par des techniques de séquencage et de PCR quantitative, les altérations moléculaires d'une série d'AHC développés chez les patients atteints de GSD. Nous avons mis en évidence que le profil des AHC développés dans un contexte de GSDI était différent de celui des AHC sporadiques, avec aucun H-AHC et une tendance vers une augmentation de la fréquence des mutations de CTNNB1. Nous avons également observé que les foies non tumoraux des patients atteints de GSDI présentaient différentes anomalies métaboliques (répression de la néoglucogenèse et activation de la glycolyse et de la synthèse des acides gras) également retrouvées dans les H-AHC sporadiques. Ces anomalies sont d'autre connues pour favoriser la cancérogénèse. Notre étude a ainsi démontré que la GSDI prédisposait à des AHC de sous type moléculaire particulier, elle a également identifié diverses anomalies métaboliques observées dans les foies non tumoraux des patients atteints de GSDI qui pourraient contribuer au développement des tumeurs. Deuxième partie: Le carcinome hépatocellulaire (CHC), développé à partir des hépatocytes, est la tumeur maligne hépatique primitive la plus fréquente. Il représente le cinquième cancer le plus fréquent dans le monde et la troisième cause de mortalité liée au cancer. Il se développe dans environ 80% des cas dans un contexte d'hépatopathie chronique, sur parenchyme cirrhotique. Le processus de transformation maligne de la cirrhose en CHC est séquentiel, et passe par différentes étapes prénéoplasiques, comme les macronodules de bas ou haut grade. Il a récemment été mis en évidence que l'anomalie moléculaire la plus fréquente dans le CHC était les mutations du promoteur de TERT, gène codant pour la télomérase. Le but de notre étude a été d'étudier si ces mutations étaient également présente dans une série de 96 nodules développés sur cirrhose. Dans 31 cas, nous avons également déterminer le statut mutationnel de 10 gènes fréquemment mutés dans le CHC. L'ensemble des nodules a fait l'objet d'une relecture par 6 anatomopathologistes spécialisés en pathologie hépatique, et l'expression de marqueurs immunohistochimiques de malignité (Glypican 3, heat Shock protein 70, Glutamine Synthetase) a été évaluée. Nous avons identifié des mutations dans 6% des macronodules de bas grade, 20% des macronodules de haut grade, et dans environ 50% des nodules transformés en CHC. L’existence de mutations était corrélée à plusieurs critères morphologiques et immunohistochimiques de malignité. Aucune mutation dans un des 10 autres gènes fréquemment mutés dans le CHC n’a été retrouvée. Nos résultats démontrent que la fréquence des mutations du promoteur de TERT augmente au cours de la carcinogénèse hépatique, et qu’il s’agit d’une anomalie très précoce qui pourrait constituer un biomarqueur d'évaluation du risque de transformation des lésions prénéoplasiques développées sur cirrhose. / First Part: Hepatocellular adenomas (HCA) are benign tumors which most often develop in young women taking oral contraceptives. They are classified as : 1) inflammatory HCA (IHCA), characterized by mutations of genes (IL6ST, GNAS, STAT3) involved in the interleukin 6 pathway; 2) HCA with biallelic inactivating mutations of HNF1A (H-HCA) ; 3) CTNNB1 mutated HCA (bAHC), which harbour a high risk of malignant transformation and 4) unclassified HCA (UHCC). Glycogen storage disease type 1 (GSD1) is a rare hereditary metabolic disease that predispose to HCE development. The main molecular studies of HCA were pervformed on sporadic cases, and the molecular profile of HCA associated to GSDI remains to be investigated. The aim of our study was to characterize, by gene sequencing and gene expression profiling, a series of HCA developed in patients with GSD1. The molecular profile of GSD1 HCA was different to that of sporadic HCA, with a lack of H-HCA and a high frequency of b-HCA. We also observed that non tumoral livers of GSD1 patients featured several metabolic alterations (gluconeogenesis repression, glycolysis and fatty acid synthesis activation) that were also observed in sporadic H-HCA and may favor carcinogenesis. Alltogether, our study demonstrated that GSD1 predispose to particular HCA subtypes and the metabolic alterations observed in non tumorl liver of GSD1 patients may contribute to tumor formation. Second Part: Hepatocellular carcinoma (HCCIt is the fifth most frequent cancer and the third cause of cancer related death worldwide. If TERT promoter mutations are, so far, the most frequent recurrent molecular alterations of HCC, genetic determinants of the early steps of carcinogenesis on cirrhosis are still poorly understood. We aimed to evaluate the occurrence of telomerase reverse transcriptase (TERT) promoter mutations in a series of 96 macrondouels developed in a cirrhotic background. For 30 cases, 10 genes frequently mutated in HCC were also screeened. Six liver pathologists reviewed all the samples, and mmunohistochemistry (IHC) analyses were performed for glypican 3, glutamine synthase, and heat shock protein 70. TERT promoter mutations were highly related to the step-wise hepatocarcinogenesis because mutations were identified in 6% of low grade dysplastic nodules, 19% of high grade dysplastic nodules, 61% of high grade nodules with foci of transformation into HCC, and 42% of small HCC. Mutations in the 10 genes recurrently mutated in HCC were only identified in 28% of the small HCC. In conclusion, Frequency of TERT promoter mutations rapidly increases during the different steps of the transformation of premalignant lesions into HCC on cirrhosis. Consequently, somatic TERT promoter mutation is a new biomarker predictive of transformation of premalignant lesions into HCC.
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Genetic variation in TERT modifies the risk of hepatocellular carcinoma in alcohol-related cirrhosis: results from a genome-wide case-control studyBuch, Stephan, Innes, Hamish, Lutz, Philipp Ludwig, Nischalke, Hans Dieter, Marquardt, Jens U., Fischer, Janett, Weiss, Karl Heinz, Rosendahl, Jonas, Marot, Astrid, Krawczyk, Marcin, Casper, Markus, Lammert, Frank, Eyer, Florian, Vogel, Arndt, Marhenke, Silke, von Felden, Johann, Sharma, Rohini, Atkinson, Stephen Rahul, McQuillin, Andrew, Nattermann, Jacob, Schafmayer, Clemens, Franke, Andre, Strassburg, Christian, Rietschel, Marcella, Altmann, Heidi, Sulk, Stefan, Thangapandi, Veera Raghavan, Brosch, Mario, Lackner, Carolin, Stauber, Rudolf E, Canbay, Ali, Link, Alexander, Reiberger, Thomas, Mandorfer, Matthias, Semmler, Georg, Scheiner, Bernhard, Datz, Christian, Romeo, Stefano, Corradini, Stefano Ginanni, Irving, William Lucien, Morling, Joanne R, Guha, Indra Neil, Barnes, Eleanor, Ansari, M Azim, Quistrebert, Jocelyn, Valenti, Luca, Müller, Sascha A, Morgan, Marsha Yvonne, Dufour, Jean-François, Trebicka, Jonel, Berg, Thomas, Deltenre, Pierre, Mueller, Sebastian, Hampe, Jochen, Stickel, Felix 22 February 2024 (has links)
Objective: Hepatocellular carcinoma (HCC) often develops in patients with alcohol-related cirrhosis at an annual risk of up to 2.5%. Some host genetic risk factors have been identified but do not account for the majority of the variance in occurrence. This study aimed to identify novel susceptibility loci for the development of HCC in people with alcohol related cirrhosis. - Design: Patients with alcohol-related cirrhosis and HCC (cases: n=1214) and controls without HCC (n=1866), recruited from Germany, Austria, Switzerland, Italy and the UK, were included in a two-stage genome-wide association study using a case–control design. A validation cohort of 1520 people misusing alcohol but with no evidence of liver disease was included to control for possible association effects with alcohol misuse. Genotyping was performed using the InfiniumGlobal Screening Array (V.24v2, Illumina) and the OmniExpress Array (V.24v1-0a, Illumina). - Results: Associations with variants rs738409 in PNPLA3 and rs58542926 in TM6SF2 previously associated with an increased risk of HCC in patients with alcohol-related cirrhosis were confirmed at genome-wide significance. A novel locus rs2242652(A) in TERT (telomerase reverse transcriptase) was also associated with a decreased risk of HCC, in the combined meta-analysis, at genome-wide significance (p=6.41×10⁻⁹, OR=0.61 (95% CI 0.52 to 0.70). This protective association remained significant after correction for sex, age, body mass index and type 2 diabetes (p=7.94×10⁻⁵, OR=0.63 (95% CI 0.50 to 0.79). Carriage of rs2242652(A) in TERT was associated with an increased leucocyte telomere length (p=2.12×10⁻⁴⁴). - Conclusion: This study identifies rs2242652 in TERT as a novel protective factor for HCC in patients with alcohol-related cirrhosis.
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Synthetic applications of chiral homoallylic sulfinamines / Aplicaciones sintéticas de homoalilsulfinaminas quiralesBosque, Irene 14 February 2014 (has links)
No description available.
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THERMODYNAMIC AND SPECTROSCOPIC ANALYSIS OF TERTBUTYL ALCOHOL HYDRATE: APPLICATION FOR THE METHANE GAS STORAGE AND TRANSPORTATIONPark, Youngjune, Cha, Minjun, Shin, Woongchul, Cha, Jong-Ho, Lee, Huen, Ripmeester, John A. 07 1900 (has links)
Recently, clathrate hydrate has attracted much attention because of its energy gas enclathration
phenomenon. Since energy gas such as methane, ethane, and hydrogen could be stored in solid
hydrate form, clathrate hydrate research has been considerably focused on energy gas storage and
transportation medium. Especially, methane hydrate, which is crystalline compound that are
formed by physical interaction between water and relatively small sized guest molecules, can
contain about as much as 180 volumes of gas at standard pressure and temperature condition. To
utilize gas hydrate as energy storage and transportation medium, two important key features:
storage capacity and storage condition must be considered. Herein, we report the inclusion
phenomena of methane occurred on tert-butyl alcohol hydrate through thermodynamic
measurement and spectroscopic analysis by using powder X-ray diffractometer, and 13C solidstate
NMR. From spectroscopic analysis, we found the formation of sII type (cubic, Fd3m)
clathrate hydrate by introducing methane gas into tert-butyl alcohol hydrate whereas tert-butyl
alcohol hydrate alone does not form clathrate hydrate structure. Under equilibrium condition,
pressure-lowering effect of methane + tert-butyl alcohol double hydrate was also observed. The
present results give us several key features for better understanding of inclusion phenomena
occurring in the complex hydrate systems and further developing methane or other gas storage
and transportation technique.
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Molecular simulation of the adsorption of organics from waterYazaydin, Ahmet Ozgur. January 2007 (has links)
Thesis (Ph. D.)--Worcester Polytechnic Institute. / Keywords: Water; Adsorption; Molecular simulation; Nanoporous materials. Includes bibliographical references (p. 117-119).
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Estratégias sintéticas para a preparação de novos fotossensibilizadores do tipo ftalocianinas / Synthetic strategies for preparation of new photosensitizers such as phthalocyaninesGobo, Nicholas Roberto da Silva 28 February 2013 (has links)
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Previous issue date: 2013-02-28 / Universidade Federal de Minas Gerais / In this work some studies about the synthesis of a new Znphthalocyanine derivative containing 8 tert-butyl groups on peripheral positions were performed. In order to obtain this compound, a new monomeric unit were synthesized 4,5-di-tert-butylphthalonitrile where a Diels-Alder reaction between a cyclic sulfone (diene) and a dinitrile (dienophile) was the key step. Beyond the synthesis and structural characterization of this phthalocyanine, preliminary photophysical studies to verify potential applications of this compound as photosensitizer were performed. To reach the 4,5-dissubstituted phthalonitrile 8, firstly, thiophene 5 was synthesized (SCHEME 8). After established the methodology to provide 5 in good yield, some tests between 5 and fumaronitrile (6) on cycloaddition conditions were performed, however, as expected, no reaction occurred, and the starting materials were recovered (SCHEME 9). Aiming at the raising diene 5 reactivity, this compound was oxidized to sulfone 9 (SCHEME 10). After that, some test between the sulfone 9 and fumaronitrile (6) were performed. The objective was to achieve a one-pot 3 steps reaction (Diels-Alder SO2 cheletropic elimination oxidation). However compound 8 was reached only in poor yields (SCHEME 10). To overcome the poor yields, some dinitrilic dienophiles were proposed. For example, dicyanoacetylene 10 (SCHEME 11) could furnish the phthalonitrile 8 after a cycloaddition and SO2 elimination. However, dicyanoacetylene (10) showed not to be accessible, and, in our hands, it was not possible to obtain with literature available procedures. According to literature, the insertion of halogens in dinitrilic dienophiles greatly raises its reactivity for cycloaddition reactions. Then, the bromination of fumaronitrile (6) to obtain the dienophile 13 was performed (SCHEME 12). After compound 13 was reached, some tests with diene 9 were done. The 4,5-di-tertbutylphthalonitrile (8) was obtained in 50% yield in a solvent-free three step domino sequence (Diels-Alder SO2 cheletropic elimination HBr elimination). Studies to obtain the phthalocyanine 14 were performed (SCHEME 13). Firstly, a current methodology in literature were tested which uses DMAE/140°C/Zn(OAc)2, however the best obtained result for 14 was only 7% yield. In addition, many polymeric byproducts were observed. Another tested methodology was the addition of phthalonitrile 8 in a solution of n-pentanol and its respective alcoxide under heating. Phthalocyanine 15 was obtained in 22% yield in these conditions. When the tetramerization was performed and the crude product metallated using anhydrous Zn(OAc)2, phthalocyanine 14 was obtained in 21% yield (SCHEME 14). In both cases these results were optimized, and the results were in agreement with the literature. All synthesized compounds were fully characterized (1D and 2D NMR, UV-Vis, IR), HRMS (ESI-TOF for compound 8 and MALDI-TOF for compounds 14 and 15) and low resolution mass spectroscopy (compounds 1, 2, 3, 4, 5 and 9). Preliminary photophysical and photochemical studies for phthalocyanines 14 and 15 were performed (aggregation studies, singlet oxygen quantum yield, fluorescence quantum yield and photobleaching). The obtained results demonstrated compounds 14 and 15 fulfill some essential requirements for PDT studies. / Neste trabalho foram realizados alguns estudos sobre a síntese de um novo derivado do tipo Zn-ftalocianina, contendo oito grupos tert-butil em suas posições periféricas. Para isso, iniciamos com a síntese de uma nova unidade monomérica - 4,5-di-tert-butilftalonitrilo - tendo como etapa chave a reação de Diels- Alder entre uma sulfona cíclica (dieno) e um dienófilo dinitrílico. Além da síntese e caracterização estrutural desta nova ftalocianina, foram realizados alguns estudos fotofísicos preliminares visando apontar algumas aplicações deste corante enquanto fotossensibilizador. Para obter o ftalonitrilo 4,5-dissubstituído, inicialmente foi realizada a síntese do tiofeno 5, como descrito no ESQUEMA 1. Estabelecida a metodologia que forneceu 5 em melhor rendimento, foram realizados alguns testes de cicloadição entre o tiofeno 5 e o fumaronitrilo (6), porém, como esperado, a reação não ocorreu, sendo possível recuperar os materiais de partida (ESQUEMA 2). Visando aumentar a reatividade do dieno 5, foi realizada uma oxidação para a sulfona 9 (ESQUEMA 3). Alguns testes de cicloadição foram realizados, utilizando a sulfona 9 e o fumaronitrilo (6). Neste caso, o objetivo foi realizar uma reação one-pot com três etapas reacionais (Diels-Alder - eliminação queletrópica de SO2 - oxidação). O composto 8 foi obtido, entretanto, apenas em baixos rendimentos (5-19%) (ESQUEMA 3). Visando contornar os baixos rendimentos de obtenção de 8, propusemos alguns outros dienófilos dinitrílicos. Por exemplo, o dicianoacetileno (10) (ESQUEMA 4), que forneceria diretamente o ftalonitrilo 8 após uma cicloadição e eliminação de SO2. Entretanto, o dicianoacetileno (10) se mostrou um composto de difícil obtenção, sendo que, em nossas mãos, não foi possível obtê-lo com o procedimento descrito na literatura. De acordo com a literatura, a inserção de halogênios em dienófilos dinitrílicos aumenta muito sua reatividade frente a reações de cicloadição. Assim, partindo dessa informação, foi realizada a bromação do fumaronitrilo (6) visando obter o dienófilo 13 (ESQUEMA 5). Após a obtenção de 13 foram realizados alguns testes fazendo reagir 13 com o dieno 9, sendo que, na ausência de solvente, obtevese o 4,5-di-tert-butilftalonitrilo (8) com 50% de rendimento em um processo one-pot de 3 etapas (Diels-Alder eliminação queletrópica de SO2 eliminação de HBr). Após realizar a síntese do ftalonitrilo 8, foram iniciados os estudos para obtenção da respectiva ftalocianina de zinco octassubstituída 14 (ESQUEMA 6). Primeiramente foram testadas algumas metodologias de uso recorrente na literatura, utilizando-se DMAE/140oC/Zn(OAc)2, entretanto, o melhor resultado de formação 14 foi de apenas 7% de rendimento, além da formação de muitos polímeros. A próxima metodologia testada foi a adição do ftalonitrilo 8 em uma solução de n-pentanol anidro e seu respectivo alcóxido de sódio, sob aquecimento (ESQUEMA 7). Nestas condições foi obtida a ftalocianina não metalada 15 com 22% de rendimento. Quando a reação de tetramerização foi realizada e o produto reacional foi submetido à metalação com Zn(OAc)2 sem purificação prévia, o composto 14 foi isolado com 21% de rendimento (ESQUEMA 7). Em ambos os casos estes foram os melhores resultados obtidos após a otimização dos procedimentos, sendo que rendimentos em torno de 20% são compatíveis com a maioria das sínteses descritas na literatura destes compostos. Os compostos sintetizados neste trabalho foram caracterizados utilizando-se técnicas de espectroscopia de RMN 1D e 2D, espectroscopia na região do UV-Vis, espectroscopia na região do infravermelho, espectrometria de massas de baixa e espectrometria de massas de alta resolução (ESI-TOF e MALDI-TOF). Estudos fotofísicos e fotoquímicos preliminares foram realizados (estudos de agregação, rendimento quântico de oxigênio singlete, rendimento quântico de fluorescência e photobleaching) para as ftalocianinas 14 e 15. Os resultados obtidos indicaram que estes novos compostos reúnem algumas das características essenciais para uso enquanto fotossensibilizador em tratamentos de lesões por terapia fotodinâmica (PDT), por exemplo, ausência de agregação em solução e produção de oxigênio singlete.
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Etude de la diversité bactérienne et génétique dans des cultures dégradant l'ETBE ou le MTBELe Digabel, Yoann 04 October 2013 (has links)
L’éthyl tert-butyl éther (ETBE) et le méthyl tert-butyl éther (MTBE) sont des éthers carburants utilisés comme additifs dans les essences sans plomb. Du fait de leur utilisation massive, de nombreux cas de pollutions d’aquifères ont été répertoriés, en particulier pour le MTBE, et ces composés représentent donc un risque sanitaire potentiel. Des travaux récents ont permis de mettre en évidence différents micro-organismes capables de dégrader ces composés malgré leur faible biodégradabilité dans l'environnement. Néanmoins, une meilleure compréhension de l'écologie et de la régulation de ces capacités de dégradation permettrait une meilleure gestion de la bioremédiation de sites contaminés par l'ETBE ou le MTBE.L’objectif de la thèse, réalisée dans le cadre d'un projet ANR Blanc (MiOxyFun), est de mieux comprendre l'écologie des communautés microbiennes impliquées dans la dégradation de ces éthers et leur relation avec la régulation ainsi qu'avec les cinétiques de dégradation de ces composés par des membres spécifiques de ces communautés. Ainsi, à partir de différents échantillons environnementaux venant de sites pollués par l'ETBE ou le MTBE, des enrichissements ont pu être réalisés en laboratoire afin d'étudier leurs microflores. Ces enrichissements ont été étudiés notamment pour leurs cinétiques de dégradation, la composition de leurs communautés bactériennes, et pour l'isolement de souches bactériennes directement impliquées dans la dégradation de ces composés. L'étude des cinétiques de dégradation de l'ETBE ou du MTBE par différents enrichissements obtenus sur ETBE (cinq) et sur MTBE (six) a permis de montrer des profils de dégradation très différents. La dégradation était généralement lente et s'accompagnait d'un faible rendement en biomasse avec parfois accumulation transitoire de tert-butanol (TBA). Les capacités de dégradation d'autres composés des essences (BTEXs et n-alcanes) étaient aussi différentes d'un enrichissement à l'autre, le benzène, entre autres, étant dégradé par 10/11 enrichissements. Des techniques d'empreinte moléculaire (RISA, DGGE) ont permis de constater que les communautés bactériennes présentes dans les cinq enrichissements sur ETBE étaient différentes de celles sur les enrichissements sur MTBE. Les enrichissements sur ETBE ont fait spécifiquement l'objet d'une étude par analyse de banques de clones réalisées à partir des gènes codant l'ARNr 16S de ces enrichissements. Cette étude a montré la prédominance des Proteobacteria dans trois enrichissements, la prédominance des Acidobacteria dans un autre ainsi qu'une composition plus héterogène dans le cinquième. De plus, des Actinobacteria ont été détectées dans les 5 enrichissements.En parallèle, plusieurs souches possédant des capacités de dégradation ont été isolées des enrichissements: Rhodococcus sp. IFP 2040, IFP 2041, IFP 2042, IFP 2043 (dégradant l'ETBE jusqu'au TBA), une Betaproteobacteria IFP 2047 (dégradant l'ETBE), Bradyrhizobium sp. IFP 2049 (dégradant le TBA), Pseudonocardia sp. IFP 2050 (dégradant l'ETBE et le MTBE), Pseudoxanthomonas sp. IFP 2051 et une Proteobacteria IFP 2052 (dégradant le MTBE). Une étude par qPCR sur les gènes codant l'ARNr 16S a montré la prédominance de certaines souches isolées dans les enrichissements ETBE. Enfin, plusieurs gènes connus comme étant impliqués dans la dégradation des éthers carburants ont pu être mis en évidence dans les enrichissements et dans certaines des souches isolées. / ETBE and MTBE are fuel oxygenates added to unleaded gasoline to improve combustion. Due to their extensive use, numerous aquifers have been contaminated, particularly by MTBE. The use of ETBE and MTBE is considered to represent an environmental risk. Recent research has uncovered a range of microorganisms capable of degrading these compounds, even though their environmental half-lives are long. Improved understanding of the ecology and regulation of this degradative ability could improve the management of the ETBE and MTBE contaminated site remediation. The aim of this work, taking place in the framework of the ANR project MiOxyFun was to investigate the ecology of ETBE- and MTBE-degrading microbial communities and their relationship to the regulation and kinetics of ETBE- and MTBE-degradation by specific members of these communities. Several ETBE- and MTBE-degrading microbial communities were enriched in the laboratory from environmental samples from contaminated sites throughout the world. These enrichments were examined for their degradation kinetics, microbial community structure, and used to isolate specific community members actively degrading ETBE and/or MTBE. The ETBE or MTBE biodegradation kinetics of the five ETBE- and six MTBE- degrading enrichments demonstrated a diversity of biodegradation rates. Overall, biodegradation was generally slow and associated to a low biomass yield. Tert-butanol (TBA) was transiently produced in several cases. Biodegradation of other gasoline compounds (BTEXs and n-alkanes) was tested and varied among the enrichments studied. Benzene, however, was degraded in 10 out of the 11 enrichments. DNA fingerprinting techniques (RISA, DGGE) showed that the microflora present in the five ETBE enrichments were different from those of the MTBE enrichments. The ETBE enrichments were studied further by sequencing the 16S rRNA genes extracted, amplified and cloned from these enrichments. Proteobacteria dominated three of the ETBE enrichments, Acidobacteria in another one, and a more heterogeneous composition was found in the fifth ETBE enrichment. Actinobacteria were detected in all five enrichments. Several strains with ETBE or MTBE degradation capacities were isolated: Rhodococcus sp. IFP 2040, IFP 2041, IFP 2042, IFP 2043 (degrading ETBE to TBA),a Betaproteobacteria IFP 2047 (degrading ETBE), Bradyrhizobium sp. IFP 2047 (degrading TBA), Pseudonocardia sp. IFP 2050 (degrading ETBE and MTBE), Pseudoxanthomonas sp. IFP 2051 and a Proteobacteria IFP 2052 (degrading MTBE). Quantification of the 16S rRNA gene confirmed the relatively high number of these isolates in some of the ETBE enrichments. Several genes involved in ETBE and/or MTBE biodegradation were detected in some of the enrichments and in some of the isolated strains.
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Revisiting aryl N-methylcarbamate acetylcholinesterase inhibitors as potential insecticides to combat the malaria-transmitting mosquito, Anopheles gambiaeHartsel, Joshua Alan 31 May 2011 (has links)
My graduate work focused on the syntheses and pharmacology of species-selective aryl methylcarbamate acetylcholinesterase inhibitors to combat the malaria-transmitting mosquito, Anopheles gambiae. We identified six novel carbamates that demonstrated levels of target selectivity exceeding our project milestone of 100-fold. Among the C2-substituted phenylcarbamates examined (class II), 2'-(2- ethylbutoxy)phenyl N-methylcarbamate (9bd*) was extraordinarily selective (570-fold ± 72). The high level of selectivity observed for many of the class II carbamates was attributed to a helical displacement within the active site of An. gambiae acetylcholinesterase, able to accommodate carbamates with larger C2-substituted secondary β-branching side chains. Conversely, this type of side chain forms unfavorable interactions within the active site of human acetylcholinesterase. The C3-substituted carbamates (class I), such as terbam (9c), were less selective than many of the class II carbamates; however, class I carbamates related to terbam (9c) were highly toxic to An. gambiae. In particular, the contact toxicity measured for 9c (LC₅₀ = 0.037 mg/mL) was equal to the commonly used agricultural insecticide, propoxur (9a, LC₅₀ = 0.037 mg/mL). In total, seventy aryl carbamates were screened for their inhibition potency and contact toxicity towards An. gambiae.
The common final step in all of these syntheses was the carbamoylation of a phenol, which normally proceeded in a 70 to 90% yield. Thirty seven novel carbamates are reported out of the seventy two prepared. Although sixteen of the phenols were commercially available, the others were prepared with known and adapted synthetic methodologies. The emerging structure-activity relationships led us to focus on the synthesis of 3-tert-alkylphenols (Class I) and 2-alkoxy or 2-alkylthio-substituted phenols (Class II). Three methods particularly stand out: First, we applied the methods of Tanaka to prepare 3-tert-alkylphenols wherein a methyl group was replaced by a trifluoromethyl group. Second, we adapted the methods of Tanaka to prepare 3-tert-alkylphenols that lack fluorine substitution. This method is competitive with the little known method of Reetz to convert aryl ketones to the corresponding 1,1-dimethylalkyl group and allows one to access electron rich tert-alkyl-substituted aromatics that are not accessible by the Friedel-Crafts alkylation (Friedel-Crafts restricted). Third, we found a convenient and high-yielding method for selective S-alkylation of 2-mercaptophenol. In addition to the synthesis of carbamates, the preparation of one hundred three intermediates, phenols, and electron rich tert-alkyl arenes are reported. / Ph. D.
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